[gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

[Hyuntae Na]

I printed all small 50 eigenvalues, and their first 9 are listed as follows as before:* -1.8476593e-06* -1.2164109e-06* -1.4830436e-07* 1.3104790e-06* 1.1364704e+00* 1.7418209e+00* 2.2836573e+00* 3.7218206e+00* 4.4875873e+00 As you see, the first three of them are negative and close to zero, which can be considered as zero. do you know any reason of this,  having only 4 (close to) zero eigenvalues ?? -- Hyuntae > Message: 3
> Date: Sun, 10 Mar 2013 23:10:05 +0100
> From: "lloyd riggs" <lloyd.riggs at gmx.ch>
> Subject: Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol
> 	for	l-bfgs)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <20130310221005.162230 at gmx.net>
> Content-Type: text/plain; charset="utf-8"
> 
> 
> I can imagine why you would go past the first few, but does it print the zero's or just negate them from the equation, as there 0?
> 
> Stephan
> -------- Original-Nachricht --------
> > Datum: Sun, 10 Mar 2013 14:34:52 -0500
> > Von: Hyuntae Na <htna at hotmail.com>
> > An: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > Betreff: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for	l-bfgs)
> 
> > Dear, This is the same issue that I asked last time. I wonder (1) if I
> > setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even
> > though the conformation of a protein is in equilibrium  in the enough degree,
> > or (2) if it gromacs does not make it in equilibrium because of the limit
> > of the tolerance that gromacs can take care of. Is there anyone who can
> > give me an advice for this? I updated the sample location in the case that the
> > previous Skype link is not available. I am studying several protein
> > fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I found
> > out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues
> > even though having 6 zero eigenvalues are expected. I tried to reduce the
> > tolerance level lesser than 10^-6 for the l-bfgs minimization, but still it
> > have only 4 zero eigenvalues. Following is the 9 smallest eigenvalues (you
> > can see that it has only 4 close-to-zero eigenvalues):
> > -1.8476593e-06-1.2164109e-06-1.4830436e-071.3104790e-061.1364704e+001.7418209e+002.2836573e+003.7218206e+004.4875873e+00
> > Theoretically, NMA should have 6 zero eigenvalues which represents the
> > freedom of the rotation and translation. I wonder why this happens.
> >  
> > Is there anyone who can help me for this problem?
> >  
> > In order to specify the case, I leave a link to download a zip file that
> > contains files for one NMA tests having the problem: script, mdp, pdb, gro,
> > topol, etc. The zip file also includes the eigenvalue/vector files.
> > http://129.186.69.109/NMA-test.zip
> >  
> > Thank you very much.
> >  
> > -- Hyuntae